Optimized DNA chip for resistance research

Press release / 18.7.2003

Freqently, single nucleotide polymorphisms (SNPs) are responsible for the formation of resistances in pathogens. Researchers at Fraunhofer IGB have optimized a DNA chip, which enables the identification of such mutations in the ERG11 gene of the human pathogenic fungus Candida albicans.

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DNA chip for analysing different gene sequences in the wild type and mutants.

Resistant pathogens are becoming an increasing problem in hospitals. One of the most common infectious germs is the pathogenic human fungus Candida albicans. In Germany alone, Candida infections kill several thousand people each year. Patients whose immune systems have been weakened as a result of chemotherapy or organ transplants are particularly badly affected. Treatment of the infections is often made more difficult by antimycotic resistance. Frequently, single nucleotide polymorphisms (SNPs) on the ERG11 gene of the fungus are responsible for the formation of such resistance.

In her prize-winning thesis, Kathrin Zeller established and optimized (with the aid of DNA chip technology) at the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB in Stuttgart, Germany, a test system that enables such individually mutated DNA building blocks and bases to be identified. The test is based on what is known as the allele-specific primer extension. This involves anchoring DNA fragments of the ERG11 gene as probes on a chip. The free ends of these probes differ and thereby represent the base variations by which a SNP mutant differs from the original wild type. The Candida strains already isolated from sick patients can now be tested on this chip. Complementary sequences from the isolates accumulate on the probes via highly-specific base pairing (hybridization). In the subsequent enzyme reaction, only those probes that fully correspond are lengthened and fluorescence-marked. The fluorescence signal on the chip indicates whether the isolated strain is a wild type or a mutant, and therefore whether or not it is resistant.

The aim of the research is the development of a clinical test kit in chip format. The pathogen strain of the infected patient can thereby be easily examined for its specific antimycotic resistance and can then be effectively treated with an effective antimycotic drug. This avoids unnecessary side effects for the patient.

“The special nature of the described work lies in the adaptation of the chip technology to the pathogenic fungus C. albicans. It also stands out in terms of a clear increase in the signal intensity. Thanks to the optimization, the amount of DNA required could be reduced to one twentieth of the original amount needed“ explains Dr. Nicole Hauser from the research group Genomics – Proteomics – Screening (headed by Dr. Steffen Rupp) at Fraunhofer IGB, in which Kathrin Zeller produced her work. The graduate of the Europa Fachhochschule Fresenius in Idstein has received the Max Buchner Prize, awarded by DECHEMA, on 25th July 2003 at this year’s university graduation ceremony.